|title: “breathtestcore: 13C breath test to analyze gastric emptying”|
|author: “Dieter Menne”|
Menne Biomed Consulting Tübingen, Germany
This is a reboot of R package dmenne/d13cbreath which is partially obsolete.
nls, which gives successful estimates for 90% of PDR curves.
nlmewhen data from multiple recordings are available, resulting in much more reliable estimates for studies.
t50BluckCowardfor a comparison with published data.
The software is being developed in cooperation with the Department of Gastroenterology of the University Hospital of Zürich and Claraspital Basel. Thanks to Benjamin Misselwitz, Mark Fox and Werner Schwizer. Special thanks to Andreas Steingötter for constantly reminding me that better statistics does necessarily make a method physiologically relevant.
To install the most recent versions of the package, use
devtools::install_github("dmenne/breathtestcore", build_vignettes = TRUE) # In case you want to use the fancy Stan-based methodes devtools::install_github("dmenne/breathteststan") # And here the web app; this is not yet on CRAN and must be installed from github devtools::install_github("dmenne/breathtestshiny", build_vignettes = TRUE)
Do not forget to use
build_vignettes = TRUE.
Stable version of the packages breathtestcore and breathteststan can also be installed from CRAN. Since packages are under strong development, we recommend to use the github versions.
The Docker image contains RStudio, package
gastempt to analyze MRI/scintigraphic gastric emptying data, and the
You can run the web app online. No data are stored, but you can download all results and a series of tests for studies.
This example is from the documentation of function nlme_fit.
library(breathtestcore) d = simulate_breathtest_data(n_records = 3, noise = 0.2, seed = 4711) data = cleanup_data(d$data) fit = nlme_fit(data) plot(fit) # calls plot.breathtestfit
For additional examples, see the documentation and the tests in folder
tests/testthat of the source package.
The core fitting functions and the Stan variants are reasonably stable and can be used to analyze your breath test data with R. The Shiny web app with reporting is work in progress; online demo, source code.
Ghoos, Y. F., B. D. Maes, B. J. Geypens, G. Mys, M. I. Hiele, P. J. Rutgeerts, and G. Vantrappen. 1993. “Measurement of Gastric Emptying Rate of Solids by Means of a Carbon-Labeled Octanoic Acid Breath Test.” Gastroenterology 104 (6). Department of Medicine, University Hospital Gasthuisberg, Belgium.: 1640–7.
Maes, B. D., B. J. Geypens, Y. F. Ghoos, M. I. Hiele, and P. J. Rutgeerts. 1998. “13C-Octanoic Acid Breath Test for Gastric Emptying Rate of Solids.” Gastroenterology 114 (4): 856–59.
Bluck LJC (2009) Recent advances in the interpretation of the 13C octanoate breath test for gastric emptying. J. Breath Res. 3, https://iopscience.iop.org/1752-7163/3/3/034002/
Bluck, LJC, Jackson S, Vlasakakis G, Mander A (2011) Bayesian hierarchical methods to interpret the 13C-octanoic acid breath test for gastric emptying. Digestion 83_96-107.